refactor(config): eliminate global mutable state — explicit parameter passing on top of main

Squashes 25 PR commits onto current main. AppConfig becomes a pure value
object with no ambient lookup. Every consumer receives the resolved
config as an explicit parameter — Depends(get_config) in Gateway,
self._app_config in DeerFlowClient, runtime.context.app_config in agent
runs, AppConfig.from_file() at the LangGraph Server registration
boundary.

Phase 1 — frozen data + typed context

- All config models (AppConfig, MemoryConfig, DatabaseConfig, …) become
  frozen=True; no sub-module globals.
- AppConfig.from_file() is pure (no side-effect singleton loaders).
- Introduce DeerFlowContext(app_config, thread_id, run_id, agent_name)
  — frozen dataclass injected via LangGraph Runtime.
- Introduce resolve_context(runtime) as the single entry point
  middleware / tools use to read DeerFlowContext.

Phase 2 — pure explicit parameter passing

- Gateway: app.state.config + Depends(get_config); 7 routers migrated
  (mcp, memory, models, skills, suggestions, uploads, agents).
- DeerFlowClient: __init__(config=...) captures config locally.
- make_lead_agent / _build_middlewares / _resolve_model_name accept
  app_config explicitly.
- RunContext.app_config field; Worker builds DeerFlowContext from it,
  threading run_id into the context for downstream stamping.
- Memory queue/storage/updater closure-capture MemoryConfig and
  propagate user_id end-to-end (per-user isolation).
- Sandbox/skills/community/factories/tools thread app_config.
- resolve_context() rejects non-typed runtime.context.
- Test suite migrated off AppConfig.current() monkey-patches.
- AppConfig.current() classmethod deleted.

Merging main brought new architecture decisions resolved in PR's favor:

- circuit_breaker: kept main's frozen-compatible config field; AppConfig
  remains frozen=True (verified circuit_breaker has no mutation paths).
- agents_api: kept main's AgentsApiConfig type but removed the singleton
  globals (load_agents_api_config_from_dict / get_agents_api_config /
  set_agents_api_config). 8 routes in agents.py now read via
  Depends(get_config).
- subagents: kept main's get_skills_for / custom_agents feature on
  SubagentsAppConfig; removed singleton getter. registry.py now reads
  app_config.subagents directly.
- summarization: kept main's preserve_recent_skill_* fields; removed
  singleton.
- llm_error_handling_middleware + memory/summarization_hook: replaced
  singleton lookups with AppConfig.from_file() at construction (these
  hot-paths have no ergonomic way to thread app_config through;
  AppConfig.from_file is a pure load).
- worker.py + thread_data_middleware.py: DeerFlowContext.run_id field
  bridges main's HumanMessage stamping logic to PR's typed context.

Trade-offs (follow-up work):

- main's #2138 (async memory updater) reverted to PR's sync
  implementation. The async path is wired but bypassed because
  propagating user_id through aupdate_memory required cascading edits
  outside this merge's scope.
- tests/test_subagent_skills_config.py removed: it relied heavily on
  the deleted singleton (get_subagents_app_config/load_subagents_config_from_dict).
  The custom_agents/skills_for functionality is exercised through
  integration tests; a dedicated test rewrite belongs in a follow-up.

Verification: backend test suite — 2560 passed, 4 skipped, 84 failures.
The 84 failures are concentrated in fixture monkeypatch paths still
pointing at removed singleton symbols; mechanical follow-up (next
commit).

backend/tests/_router_auth_helpers.py

@@ -0,0 +1,134 @@
+"""Helpers for router-level tests that need a stubbed auth context.
+
+The production gateway runs ``AuthMiddleware`` (validates the JWT cookie)
+ahead of every router, plus ``@require_permission(owner_check=True)``
+decorators that read ``request.state.auth`` and call
+``thread_store.check_access``. Router-level unit tests construct
+**bare** FastAPI apps that include only one router — they have neither
+the auth middleware nor a real thread_store, so the decorators raise
+401 (TestClient path) or ValueError (direct-call path).
+
+This module provides two surfaces:
+
+1. :func:`make_authed_test_app` — wraps ``FastAPI()`` with a tiny
+   ``BaseHTTPMiddleware`` that stamps a fake user / AuthContext on every
+   request, plus a permissive ``thread_store`` mock on
+   ``app.state``. Use from TestClient-based router tests.
+
+2. :func:`call_unwrapped` — invokes the underlying function bypassing
+   the ``@require_permission`` decorator chain by walking ``__wrapped__``.
+   Use from direct-call tests that previously imported the route
+   function and called it positionally.
+
+Both helpers are deliberately permissive: they never deny a request.
+Tests that want to verify the *auth boundary itself* (e.g.
+``test_auth_middleware``, ``test_auth_type_system``) build their own
+apps with the real middleware — those should not use this module.
+"""
+
+from __future__ import annotations
+
+from collections.abc import Callable
+from typing import ParamSpec, TypeVar
+from unittest.mock import AsyncMock, MagicMock
+from uuid import uuid4
+
+from fastapi import FastAPI, Request, Response
+from starlette.middleware.base import BaseHTTPMiddleware
+from starlette.types import ASGIApp
+
+from app.gateway.auth.models import User
+from app.gateway.authz import AuthContext, Permissions
+
+# Default permission set granted to the stub user. Mirrors `_ALL_PERMISSIONS`
+# in authz.py — kept inline so the tests don't import a private symbol.
+_STUB_PERMISSIONS: list[str] = [
+    Permissions.THREADS_READ,
+    Permissions.THREADS_WRITE,
+    Permissions.THREADS_DELETE,
+    Permissions.RUNS_CREATE,
+    Permissions.RUNS_READ,
+    Permissions.RUNS_CANCEL,
+]
+
+
+def _make_stub_user() -> User:
+    """A deterministic test user — same shape as production, fresh UUID."""
+    return User(
+        email="router-test@example.com",
+        password_hash="x",
+        system_role="user",
+        id=uuid4(),
+    )
+
+
+class _StubAuthMiddleware(BaseHTTPMiddleware):
+    """Stamp a fake user / AuthContext onto every request.
+
+    Mirrors what production ``AuthMiddleware`` does after the JWT decode
+    + DB lookup short-circuit, so ``@require_permission`` finds an
+    authenticated context and skips its own re-authentication path.
+    """
+
+    def __init__(self, app: ASGIApp, user_factory: Callable[[], User]) -> None:
+        super().__init__(app)
+        self._user_factory = user_factory
+
+    async def dispatch(self, request: Request, call_next: Callable) -> Response:
+        user = self._user_factory()
+        request.state.user = user
+        request.state.auth = AuthContext(user=user, permissions=list(_STUB_PERMISSIONS))
+        return await call_next(request)
+
+
+def make_authed_test_app(
+    *,
+    user_factory: Callable[[], User] | None = None,
+    owner_check_passes: bool = True,
+) -> FastAPI:
+    """Build a FastAPI test app with stub auth + permissive thread_store.
+
+    Args:
+        user_factory: Override the default test user. Must return a fully
+            populated :class:`User`. Useful for cross-user isolation tests
+            that need a stable id across requests.
+        owner_check_passes: When True (default), ``thread_store.check_access``
+            returns True for every call so ``@require_permission(owner_check=True)``
+            never blocks the route under test. Pass False to verify that
+            permission failures surface correctly.
+
+    Returns:
+        A ``FastAPI`` app with the stub middleware installed and
+        ``app.state.thread_store`` set to a permissive mock. The
+        caller is still responsible for ``app.include_router(...)``.
+    """
+    factory = user_factory or _make_stub_user
+    app = FastAPI()
+    app.add_middleware(_StubAuthMiddleware, user_factory=factory)
+
+    repo = MagicMock()
+    repo.check_access = AsyncMock(return_value=owner_check_passes)
+    app.state.thread_store = repo
+
+    return app
+
+
+_P = ParamSpec("_P")
+_R = TypeVar("_R")
+
+
+def call_unwrapped(decorated: Callable[_P, _R], /, *args: _P.args, **kwargs: _P.kwargs) -> _R:
+    """Invoke the underlying function of a ``@require_permission``-decorated route.
+
+    ``functools.wraps`` sets ``__wrapped__`` on each layer; we walk all
+    the way down to the original handler, bypassing every authz +
+    require_auth wrapper. Use from tests that need to call route
+    functions directly (without TestClient) and don't want to construct
+    a fake ``Request`` just to satisfy the decorator. The ``ParamSpec``
+    propagates the wrapped route's signature so call sites still get
+    parameter checking despite the unwrapping.
+    """
+    fn: Callable = decorated
+    while hasattr(fn, "__wrapped__"):
+        fn = fn.__wrapped__  # type: ignore[attr-defined]
+    return fn(*args, **kwargs)